chr19-10124423-G-C

Variant names:

• chr19-10124423-G-C
• rs11085587

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.482 in 151,892 control chromosomes in the GnomAD database, including 17,859 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.48 (17859 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.482 AC: 73215 AN: 151774 Hom.: 17868 Cov.: 31

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.510

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.513

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.482 AC: 73233 AN: 151892 Hom.: 17859 Cov.: 31 AF XY: 0.482 AC XY: 35790 AN XY: 74196

Gnomad4 AFR AF: 0.458

Gnomad4 AMR AF: 0.509

Gnomad4 ASJ AF: 0.457

Gnomad4 EAS AF: 0.333

Gnomad4 SAS AF: 0.500

Gnomad4 FIN AF: 0.483

Gnomad4 NFE AF: 0.502

Gnomad4 OTH AF: 0.508

Alfa AF: 0.494 Hom.: 2271

Bravo AF: 0.486

Asia WGS AF: 0.425 AC: 1479 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.3
DANN	Benign	0.35

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11085587; hg19: chr19-10235099;